CAMBRIDGE, UK — BlueGnome, a provider of arrays, software, and fluorescent in situ hybridization probes for research use, will later this month launch a new software package designed to meet the needs of cytogenetics laboratories.
Called DecisionTrack, the new software platform is an upgrade to BlueGnome's existing BlueFuse Multi software, and provides a framework for laboratories to mine their own data, and, ultimately, pool data from other laboratories, according to the firm.
Researchers currently use BlueGnome's products to analyze constitutional samples to elucidate genetic disease, investigate hematological malignancies, and to perform aneuploidy screens of single cells.
The release of the new software comes at a time when BlueGnome has been adding sales personnel in Europe and North America to deal with its customers in the cytogenetics community. As part of that expansion, the firm also plans to establish itself in the US later this year.
BlueGnome CEO Nick Haan told BioArray News last week that the firm plans to incorporate in the US this year and open an office, though it has not decided where it will incorporate, or when the office would open.
Haan also said that the privately held company's headcount has grown by 30 percent over the past year. He declined to elaborate.
According to BlueGnome, the new DecisionTrack software makes curated annotation information available from online databases, along with detailed information from previous array comparative genomic hybridization cases in order to support "informed and audited decisions on which imbalances are potentially pathogenic and which are probably benign."
The company's BlueFuse algorithms generate an initial list of imbalances, ordered by significance. As each imbalance is selected, DecisionTrack displays relevant information on the region using a series of color-coded tracks.
Tracks currently available include gene tracks, which enable access to online databases to explore the function of genes and their possible links to the phenotype; sample tracks, which provide access to the phenotypes of samples sharing common imbalances; CNV tracks, which highlight where copy number variation has been reported in the general population; and custom tracks, which can be loaded by the customer and, for example, can be extended to include anonymized results from labs working together in a consortium.
BlueGnome currently sells bacterial artificial chromosome and oligonucleotide arrays manufactured by Agilent Technologies for research use by cytogeneticists. The shop is currently fighting with Affymetrix, Illumina, Roche NimbleGen, Oxford Gene Technology, and others, for a slice of a market Illumina CEO Jay Flatley has referred to as "huge" (see BAN 11/18/2008).
According to several BlueGnome officials, the firm's informatics expertise could give it an advantage over its competitors. "The key to our offering is that we are not a platform company," said Graham Snudden, BlueGnome's vice president of engineering. Snudden spoke with BioArray News during a site visit to BlueGnome's headquarters here last week.
"We are perceived by the customers as platform neutral. We don't come in and say, 'We've got a platform and if we tweak it the right way, it just might meet your needs,'" Snudden said. "We start the other way and ask what they really need to make right decisions. We'll find the right platform, wrap it up in software, and deliver it with a bow on top, saying, 'This is what you require.'"
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According to Haan, software is central to BlueGnome's approach to the market. "We began life as a software company, and so we have always felt that software and the process of analyzing data and information is critical," Haan told BioArray News last week at the company's headquarters.
"Rather than coming along with a great piece of hardware and a nice microarray, and as an afterthought think that we really ought to bolt some software on it, we instead start with the software and user workflow and then add the right arrays and protocols around that," he added.
Last year, BlueGnome began offering oligo arrays in addition to its BAC CytoChip offering, and Haan said that pushing the firm's software into the oligo space was a "natural step" for the company (see BAN 12/2/2008).
"A number of people on our staff have worked on analysis and manufacture of oligo arrays in the past, so we had a great level of oligo expertise already. We also had advanced statistical methods that are applicable to both oligos and BACs," he said.
Snudden said that BlueGnome's customers currently consist of "two distinct groups:" "medium-sized cyto labs that are getting into arrays" and "those that have been running arrays for enough time to realize that to get to the next stage in data management, they have got to put in a more sophisticated data management structure within their lab.
"If you are going to run 50 samples, then you can typically manage with Excel spreadsheets and so on," Snudden said. "But if you are going to run 1,000 samples per year, then how are you going to manage with things like archiving and retrieval?"
Snudden said that higher-throughput labs are faced with the dilemma of having invested "thousands of dollars running hundreds of samples, but they are still unable to answer a simple question like, ‘Show me all the cases that have this deleted.' The best they have is paper records of their reported samples," he said.
To tap into this perceived need on the part of cytogeneticists, BlueGnome built DecisionTrack on its existing centralized database functionality. "Once you have got the data centralized, there are a few things you can do with it," said Snudden. "The first thing is use your other cohorts to interpret the sample you are currently dealing with." According to Snudden, this allows multiple lab technicians at different locations to track the processing of a sample over time.
Secondly, Snudden said that BlueGnome is increasingly trying to serve consortiums. "Think about it: There are thousands of arrays being run each year, and yet nobody has put the infrastructure in place to share this kind of information," he said.
While BlueGnome slugs it out in the cyto market, Snudden said that it is unlikely that that market would behave like the gene-expression array market, which has been marked by the departure of a number of players and the wide adoption of a handful of platforms.
"I don't think you are going to see consolidation down to one platform," Snudden said. "I mean, Agilent is pretty much the standard as an underlying platform, and whether that is a direct sale or through someone like us, it might capture around 70 percent of the market. But I think there is room for all the players."